I have two ferrets and one of them is really good and poops where she is supposed to but the male ferret has been pooping on two of the three shelves in their cage. I tried to deter him by putting food bowls on both of those shelves and then they have water on the third one. He seemed to only eat from the top shelf and still pooped on the bottom one. Then, today he also pooped on the top one! I thought ferrets didn't do that! I feel like he is being spiteful, I have been cleaning their litter and the bottom of their cage daily to avoid this but he still insists on pooping on shelves! What else can I do?

Thanks!

for potty training in the cage. 

Bring your ferrets down to one level (no shelves).
Place litter box in one corner
Food and water in the other corners.  (make sure you cover ALL your corners in the cage)

You can hang a hammock so that they have something to sleep in.  Leave them in this setup until they start using the litterbox.

Posting a picture of your cage setup will also give members some ideas to help you.